1L8N

The 1.5A crystal structure of alpha-D-glucuronidase from Bacillus stearothermophilus T-1, complexed with 4-O-methyl-glucuronic acid and xylotriose

• PDB DOI: https://doi.org/10.2210/pdb1L8N/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-03-21 Released: 2003-03-21 
• Deposition Author(s): Golan, G., Shallom, D., Teplitsky, A., Zaide, G., Shulami, S., Baasov, T., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.172 
• R-Value Work: 0.140 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.36 kDa 
• Atom Count: 6,401 
• Modelled Residue Count: 671 
• Deposited Residue Count: 679 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-D-GLUCURONIDASE	A	679	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: AGUA EC: 3.2.1.139
UniProt
Find proteins for Q8VVD2 (Geobacillus stearothermophilus) Explore Q8VVD2  Go to UniProtKB:  Q8VVD2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G87728WL GlyCosmos:  G87728WL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCW	C [auth A]	4-O-methyl-beta-D-glucopyranuronic acid C7 H12 O7 WGLLPAPKWFDHHV-RLZVPWTLSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116	B	4beta-beta-xylobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.172 
• R-Value Work: 0.140 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.946	α = 90
b = 73.946	β = 90
c = 331.341	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
SHELXL-97	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-21 
Deposition Author(s): Golan, G., Shallom, D., Teplitsky, A., Zaide, G., Shulami, S., Baasov, T., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2003-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary